.TH g_rms 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_rms - calculates rmsd's with a reference structure and rmsd matrices

.B VERSION 4.5
.SH SYNOPSIS
\f3g_rms\fP
.BI "\-s" " topol.tpr "
.BI "\-f" " traj.xtc "
.BI "\-f2" " traj.xtc "
.BI "\-n" " index.ndx "
.BI "\-o" " rmsd.xvg "
.BI "\-mir" " rmsdmir.xvg "
.BI "\-a" " avgrp.xvg "
.BI "\-dist" " rmsd\-dist.xvg "
.BI "\-m" " rmsd.xpm "
.BI "\-bin" " rmsd.dat "
.BI "\-bm" " bond.xpm "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-tu" " enum "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-what" " enum "
.BI "\-[no]pbc" ""
.BI "\-fit" " enum "
.BI "\-prev" " int "
.BI "\-[no]split" ""
.BI "\-skip" " int "
.BI "\-skip2" " int "
.BI "\-max" " real "
.BI "\-min" " real "
.BI "\-bmax" " real "
.BI "\-bmin" " real "
.BI "\-[no]mw" ""
.BI "\-nlevels" " int "
.BI "\-ng" " int "
.SH DESCRIPTION
\&g_rms compares two structures by computing the root mean square
\&deviation (RMSD), the size\-independent 'rho' similarity parameter
\&(rho) or the scaled rho (rhosc), 
\&see Maiorov & Crippen, PROTEINS \fB 22\fR, 273 (1995).
\&This is selected by \fB \-what\fR.

Each structure from a trajectory (\fB \-f\fR) is compared to a
\&reference structure. The reference structure
\&is taken from the structure file (\fB \-s\fR).


\&With option \fB \-mir\fR also a comparison with the mirror image of
\&the reference structure is calculated.
\&This is useful as a reference for 'significant' values, see
\&Maiorov & Crippen, PROTEINS \fB 22\fR, 273 (1995).


\&Option \fB \-prev\fR produces the comparison with a previous frame
\&the specified number of frames ago.


\&Option \fB \-m\fR produces a matrix in \fB .xpm\fR format of
\&comparison values of each structure in the trajectory with respect to
\&each other structure. This file can be visualized with for instance
\&\fB xv\fR and can be converted to postscript with \fB xpm2ps\fR.


\&Option \fB \-fit\fR controls the least\-squares fitting of
\&the structures on top of each other: complete fit (rotation and
\&translation), translation only, or no fitting at all.


\&Option \fB \-mw\fR controls whether mass weighting is done or not.
\&If you select the option (default) and 
\&supply a valid tpr file masses will be taken from there, 
\&otherwise the masses will be deduced from the atommass.dat file in
\&the GROMACS library directory. This is fine for proteins but not
\&necessarily for other molecules. A default mass of 12.011 amu (Carbon)
\&is assigned to unknown atoms. You can check whether this happend by
\&turning on the \fB \-debug\fR flag and inspecting the log file.


\&With \fB \-f2\fR, the 'other structures' are taken from a second
\&trajectory, this generates a comparison matrix of one trajectory
\&versus the other.


\&Option \fB \-bin\fR does a binary dump of the comparison matrix.


\&Option \fB \-bm\fR produces a matrix of average bond angle deviations
\&analogously to the \fB \-m\fR option. Only bonds between atoms in the
\&comparison group are considered.
.SH FILES
.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-f2" " traj.xtc" 
.B Input, Opt.
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-o" " rmsd.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-mir" " rmsdmir.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-a" " avgrp.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-dist" " rmsd\-dist.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-m" " rmsd.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.BI "\-bin" " rmsd.dat" 
.B Output, Opt.
 Generic data file 

.BI "\-bm" " bond.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-tu"  " enum" " ps" 
 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-what"  " enum" " rmsd" 
 Structural difference measure: \fB rmsd\fR, \fB rho\fR or \fB rhosc\fR

.BI "\-[no]pbc"  "yes   "
 PBC check

.BI "\-fit"  " enum" " rot+trans" 
 Fit to reference structure: \fB rot+trans\fR, \fB translation\fR or \fB none\fR

.BI "\-prev"  " int" " 0" 
 Compare with previous frame

.BI "\-[no]split"  "no    "
 Split graph where time is zero

.BI "\-skip"  " int" " 1" 
 Only write every nr\-th frame to matrix

.BI "\-skip2"  " int" " 1" 
 Only write every nr\-th frame to matrix

.BI "\-max"  " real" " \-1    " 
 Maximum level in comparison matrix

.BI "\-min"  " real" " \-1    " 
 Minimum level in comparison matrix

.BI "\-bmax"  " real" " \-1    " 
 Maximum level in bond angle matrix

.BI "\-bmin"  " real" " \-1    " 
 Minimum level in bond angle matrix

.BI "\-[no]mw"  "yes   "
 Use mass weighting for superposition

.BI "\-nlevels"  " int" " 80" 
 Number of levels in the matrices

.BI "\-ng"  " int" " 1" 
 Number of groups to compute RMS between

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
